Is there an easy way to find all the books with Calibre generated covers?

Easy? No.
But I'm cleaning up a huge library and had to find a better way than going through each entry one by one.
What I did was use VisiPics, a free duplicate image detector, and ran it against (a backup of) my library set loosely enough that it grouped all the Calibre and most the other generic covers together. Then I deleted all the files in those groups.
But Calibre still saw them as having a cover. So I used "Copy to library" to move them all to a new library which updated their cover status (This can be done easier via Library Maintenance. I was also merging dupes as well.) From there, running a search for "cover:false" showed me all the files I needed to generate covers for.

Not a perfect way to do it by any means, and be sure to use a backup of the library as it's very easy to seriously break stuff when playing with library files outside of Calibre, but it worked for me.